[Bioperl-l] GenBank entries creation dates
cjfields at uiuc.edu
Mon Apr 7 11:46:01 EDT 2008
Strangely enough, if you use NCBI's esummary you can get both dates.
Via Bio::DB::EUtilities in bioperl-live, if you dump out DocSum data
(using a debugging method I added in a while back):
# for multiple IDs use an array ref; also only use GI's (not accessions)
my $factory = Bio::DB::EUtilities->new(
-eutil => 'esummary',
-db => 'protein',
-id => 1621261);
One gets the following tag/value pairs:
Title :PROBABLE PYRIMIDINE OPERON REGULATORY PROTEIN
PYRR [Mycobacterium tuberculosis
I'll add in a method to grab the data element by tag (in this case,
grab the creation date by asking for the 'CreateDate' key). Might
come in handy for scripts.
On Apr 7, 2008, at 7:48 AM, Heikki Lehvaslaiho wrote:
> You probably know this but:
> - Your entry example below is a GenPept entry, not a GenBank entry
> - The NCBI sequence format "genbank" has only the last modified date.
> I do not know about other formats (ASN.1, ...)
> - NCBI Entrez is a great tool but it obscures the source database.
> - If you really are working on real GenBank entries, you can use the
> number to see find corresponding EMBL (and Swiss-Prot) flat file
> formats that
> have both creation and last modified dates.
> Post to the list if you have trouble getting the dates from EMBL/
> formats using bioperl.
> On Monday 07 April 2008 12:12:58 Miguel Pignatelli wrote:
>> Hi all,
>> Is there any way to obtain the date of creation of individual GenBank
>> entries? I don't mean the "last revision" date that can be found in
>> first line of a GenBank file.
>> I can access this creation date by looking at the "revision
>> history" of
>> any GenBank entry (for example, see
>> but I need a systematic (and local=fast) way to access this
>> Any help would be very appreciated,
>> Thank you very much in advance,
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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